Only count cells that contain nuclei (or holes in the binarized image)

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Only count cells that contain nuclei (or holes in the binarized image)

kirbyfloss
Hi - is there a way to only count the cells in the attached binarized image that contain "holes"?


I am trying to analyze slides with muscle stained with H&E - and would like to count the number of regenerating muscle fibers, which are distinguished by dark nuclei in the interior of the cell bodies (rather than on the periphery).

This is the pipeline I have set up thus far:
1) Apply colour deconvolution (using plugin by G. Landini)
2) Set threshold to binarize the resulting image in channel 2
3) Analyze particles

This works reasonably well to count all the cells in an image, but is there any way to only count the cells that contain a hole (or multiple holes) automatically? I'm aware of more manual tools, like Cell Counter, but was hoping for the most automated solution possible.

Thanks!
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Re: Only count cells that contain nuclei (or holes in the binarized image)

G. Esteban Fernandez
I'd run Analyze Particles WITHOUT "Include holes" then again WITH
"Include holes" activated and compare the Results to count the ones
for which the Area changed.

-Esteban

On Thu, Oct 15, 2015 at 8:38 AM, kirbyfloss <[hidden email]> wrote:

> Hi - is there a way to only count the cells in the attached binarized image
> that contain "holes"?
> <http://imagej.1557.x6.nabble.com/file/n5014650/workingCopy.png>
>
> I am trying to analyze slides with muscle stained with H&E - and would like
> to count the number of regenerating muscle fibers, which are distinguished
> by dark nuclei in the interior of the cell bodies (rather than on the
> periphery).
>
> This is the pipeline I have set up thus far:
> 1) Apply colour deconvolution (using plugin by G. Landini)
> 2) Set threshold to binarize the resulting image in channel 2
> 3) Analyze particles
>
> This works reasonably well to count all the cells in an image, but is there
> any way to only count the cells that contain a hole (or multiple holes)
> automatically? I'm aware of more manual tools, like Cell Counter, but was
> hoping for the most automated solution possible.
>
> Thanks!
>
>
>
> --
> View this message in context: http://imagej.1557.x6.nabble.com/Only-count-cells-that-contain-nuclei-or-holes-in-the-binarized-image-tp5014650.html
> Sent from the ImageJ mailing list archive at Nabble.com.
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html

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Re: Only count cells that contain nuclei (or holes in the binarized image)

G. Esteban Fernandez
Also, solidity is higher if there are no holes.  Maybe there's a
cutoff Solidity value above which are all your nuclei without holes,
so you would be able to run Analyze Particles with Shape Descriptors
activated (under Analyze > Set Measurements) and just see how many
nuclei there are above your cutoff Solidity (sort the list by Solidity
in Excel).

-Esteban

On Thu, Oct 15, 2015 at 10:13 AM, G. Esteban Fernandez
<[hidden email]> wrote:

> I'd run Analyze Particles WITHOUT "Include holes" then again WITH
> "Include holes" activated and compare the Results to count the ones
> for which the Area changed.
>
> -Esteban
>
> On Thu, Oct 15, 2015 at 8:38 AM, kirbyfloss <[hidden email]> wrote:
>> Hi - is there a way to only count the cells in the attached binarized image
>> that contain "holes"?
>> <http://imagej.1557.x6.nabble.com/file/n5014650/workingCopy.png>
>>
>> I am trying to analyze slides with muscle stained with H&E - and would like
>> to count the number of regenerating muscle fibers, which are distinguished
>> by dark nuclei in the interior of the cell bodies (rather than on the
>> periphery).
>>
>> This is the pipeline I have set up thus far:
>> 1) Apply colour deconvolution (using plugin by G. Landini)
>> 2) Set threshold to binarize the resulting image in channel 2
>> 3) Analyze particles
>>
>> This works reasonably well to count all the cells in an image, but is there
>> any way to only count the cells that contain a hole (or multiple holes)
>> automatically? I'm aware of more manual tools, like Cell Counter, but was
>> hoping for the most automated solution possible.
>>
>> Thanks!
>>
>>
>>
>> --
>> View this message in context: http://imagej.1557.x6.nabble.com/Only-count-cells-that-contain-nuclei-or-holes-in-the-binarized-image-tp5014650.html
>> Sent from the ImageJ mailing list archive at Nabble.com.
>>
>> --
>> ImageJ mailing list: http://imagej.nih.gov/ij/list.html

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Re: Only count cells that contain nuclei (or holes in the binarized image)

gankaku
In reply to this post by kirbyfloss
Hi kirbyfloss,

you can have a look at the "Binary Feature Extractor" in the BioVoxxel
Toolbox (http://imagej.net/BioVoxxel_Toolbox).
In the case you have a nuclear counterstain you can extract that one and
extract cells which have those nuclei and compare it to all extracted cells.

Or, as Esteban pointed out by referring to the solidity, the Extended
Particle Analyzer together with the Shape Descriptor Maps might give you a
tool at hand to separate specific shapes from each other.

Kind regards,
Jan

2015-10-15 17:38 GMT+02:00 kirbyfloss <[hidden email]>:

> Hi - is there a way to only count the cells in the attached binarized image
> that contain "holes"?
> <http://imagej.1557.x6.nabble.com/file/n5014650/workingCopy.png>
>
> I am trying to analyze slides with muscle stained with H&E - and would like
> to count the number of regenerating muscle fibers, which are distinguished
> by dark nuclei in the interior of the cell bodies (rather than on the
> periphery).
>
> This is the pipeline I have set up thus far:
> 1) Apply colour deconvolution (using plugin by G. Landini)
> 2) Set threshold to binarize the resulting image in channel 2
> 3) Analyze particles
>
> This works reasonably well to count all the cells in an image, but is there
> any way to only count the cells that contain a hole (or multiple holes)
> automatically? I'm aware of more manual tools, like Cell Counter, but was
> hoping for the most automated solution possible.
>
> Thanks!
>
>
>
> --
> View this message in context:
> http://imagej.1557.x6.nabble.com/Only-count-cells-that-contain-nuclei-or-holes-in-the-binarized-image-tp5014650.html
> Sent from the ImageJ mailing list archive at Nabble.com.
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>



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